[Bioperl-l] seqs, seqfeatures, locations etc

Johnston, Caroline Caroline.Johnston at iop.kcl.ac.uk
Wed Sep 10 11:43:26 EDT 2008


I'm trying to get my head around the various classes for storing sequences, features and locations and was hoping someone could give me some implementation advice:

I've got a Bio::EnsEMBL::Slice and I want to turn it into a Bio::Seq or SeqFeature object, with Bio::SeqFeature;:Gene::GeneStructure/Transcript/Exon info attached. I can create a Bio::Seq fine, but I also need to keep track of the chromosomal co-ordinates (chr, start, end, species, strand, genome release, database name) and I can't figure out how to store this in Bioperl. I was thinking that what I needed was some extension of a standard Bio::Seq to have genome-coordinate data attached and associated methods to translate the SeqFeature positions (relative to the Bio::Seq) to genome positions. I guess it's probably already possible to store this type of info in some collection of Bioperl objects, but between Bioperl and the EnsEMBL API I'm getting lost in perl modules. Can someone point me in the right direction?


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